Don,
IMHO, 240.21(C)(1) indicates that the secondary conductors from a multiphase transformer cannot be soley protected by the primary of the transformer. So that means that secondary protection is required.
Jim,
I agree that note 2 allows multiple ocpd's but their summed total of the ratings cannot exceed that of a single device if it were provided.
450.3 is not about protecting the transformer secondary, it is about protecting the primary.
The OP did not mention what size transformer they have nor the conductor lengths, so it is hard to give an absolute answer.
The concept of one transformer feeding two different panels may be compliant under 240.21(C)2 and 240.21(C)5 as long as there is a single device at the end of each conductor/circuit. 240.21(C)(3) allows multiple devices at the end of the conductors.
The OP is using a 100A and a 200A device so the combined protection is 300A.
Now goto the transformer.
450.3(B) says the transformer needs to be protected on the primary by 125% maximum. If the OP's 100A device meets this requirement (which it would for a 75kVA or larger 480V primary transformer), then no further investigation is needed and the installation meets the NEC.
However, if the 100A device is larger than 125% and not larger than 250%of the primary (which would be the case for a 30-45kVA transformer), the combined secondary protection could not be larger than 250% of the secondary current (100A or 150A respectively), which means the installation would not be "per code".